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- PDB-4chm: Structure of Inner Membrane Complex (IMC) Sub-compartment Protein... -

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Basic information

Entry
Database: PDB / ID: 4chm
TitleStructure of Inner Membrane Complex (IMC) Sub-compartment Protein 1 (ISP1) from Toxoplasma gondii
ComponentsIMC SUB-COMPARTMENT PROTEIN ISP1
KeywordsCELL CYCLE / CELL DIVISION / ENDODYOGENY / PLECKSTRIN HOMOLOGY (PH) FOLD
Function / homologyISP1 C-terminal / ISP1 C-terminal / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta / IMC sub-compartment protein ISP1 / IMC sub-compartment protein ISP1
Function and homology information
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsTonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Inner Membrane Complex Sub-Compartment Proteins Critical for Replication of the Apicomplexan Parasite Toxoplasma Gondii Adopt a Pleckstrin Homology Fold
Authors: Tonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J.
History
DepositionDec 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMC SUB-COMPARTMENT PROTEIN ISP1
B: IMC SUB-COMPARTMENT PROTEIN ISP1
C: IMC SUB-COMPARTMENT PROTEIN ISP1
D: IMC SUB-COMPARTMENT PROTEIN ISP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,72118
Polymers55,3764
Non-polymers1,34514
Water4,900272
1
A: IMC SUB-COMPARTMENT PROTEIN ISP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2285
Polymers13,8441
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IMC SUB-COMPARTMENT PROTEIN ISP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2285
Polymers13,8441
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IMC SUB-COMPARTMENT PROTEIN ISP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2285
Polymers13,8441
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: IMC SUB-COMPARTMENT PROTEIN ISP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0363
Polymers13,8441
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.110, 81.090, 120.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
IMC SUB-COMPARTMENT PROTEIN ISP1


Mass: 13844.036 Da / Num. of mol.: 4 / Fragment: PH FOLD CORE DOMAIN, RESIDUES 58-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: ME49 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: S8GCI7, UniProt: B9PKK4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.542
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.1→29.09 Å / Num. obs: 33884 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→28.15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.2 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25563 1716 5.1 %RANDOM
Rwork0.20346 ---
obs0.20614 32114 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.985 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 70 272 4178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193973
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.0115387
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94424.691162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89815753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0331529
X-RAY DIFFRACTIONr_chiral_restr0.1150.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 117 -
Rwork0.231 2151 -
obs--100 %

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